Seeing Double: USU Biologist Carl Rothfels is Developing Novel Polyploid Phylogenetics Tools

Humans have 23 pairs of chromosomes and 46 total chromosomes. Half come from your mother and the other half come from your father. We’re a diploid species, meaning most of our chromosomes come in matched sets.

Plants are a different story. Unlike in animals, polyploidy — having more than two sets of chromosomes — is very common among plants.

Polyploidy, says Utah State University plant biologist Carl Rothfels, is a dominant feature of existing plant species and appears to be a driver of plant diversity. Advances in genomics techniques, including CRISPR, are fueling study of the phenomenon, he says, yet polyploid phylogenetics, the study of the evolutionary history and relationships among and within polyploid plant groups, lags behind.

Rothfels was awarded a National Science Foundation Faculty Early Career Development Program (CAREER) grant to develop phylogenetic tools and apply them to the fern family Cystopteridaceae, including fragile fern and oak fern, commonly found in the Intermountain West.

“This plant family provides an excellent system for investigating big questions about polyploidy and its role in evolution and diversity,” says Rothfels, director of USU’s Intermountain Herbarium and associate professor in the Department of Biology and USU Ecology Center. “Is polyploidy an important generator of diversity and thus an engine of evolutionary success? Or, is it an evolutionary ‘dead end,’ forming new species that go extinct more quickly?”

Unraveling these mysteries is a formidable task, he says, involving collection of hard-to-get data and developing, from the ground up, complex analytical tools.

“When evolution happens in a purely branching way, you can construct a family tree,” Rothfels says. “But polyploids mess up this system and make it harder because many polyploids are also hybrids, so their history is more of a reticulated network — a web of life instead of a tree of life.”

He explains three primary steps involved in a polypoid phylogenetics study — none of which is simple and all of which present their own challenges.

The first step involves sequencing each copy of the target locus — or set of loci — present in a polyploid sample, and accurately reconstructing each distinct sequence from each subgenome.

The second step is to determine which subgenome each copy came from so that subgenome histories can be accurately reconstructed.

Step three, for which Rothfels is developing mathematical model, requires inferring polyploid evolutionary histories, which twist and turn in unexpected paths.

In pursuit of these aims, Rothfels is enlisting data collection help from an army of students and citizen scientists through the online iNaturalist network, along with a newly established annual botany trip known as the Intermountain Botanical Foray.

“We held our first foray in June 2023, and the plan is to hold this yearly trip, open to plant-fans of all walks of life, in a different Intermountain location each year,” he says. “This past year, we visited the Desert Experimental Range in Millard County in southwestern Utah, where we logged more than 1,500 iNaturalist observations covering more than 200 species of plants.”

In tandem with this effort, Rothfels is developing a curriculum in field botany to foster undergraduate learning, which he has introduced to students from USU Blanding who are participants in the yearly Native American Summer Mentorship Program.

“Our lab is working with USU’s NASMP and MESAS — Mentoring and Encouraging Student Academic Success — programs, to get students involved in study of plants, including Indigenous knowledge,” he says. “Our research is a collective effort, but not just on scientific progress, but on community building as well.”